RCPedia: Rtcs

Summary

Retrocopy Name	FCF1P3	Plot displaying the genomic locations of a retrocopy (in chr3) and its respective parental gene (in chr14). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr3:106848655-106849750 UCSC
Coordinates (T2T)	chr3:109568519-109569613 UCSC
Coordinates (hg19)	chr3:106567502-106568597 UCSC
Strand	+
Parental Sequence	NM_015962.5
Parental seq. overlap	697 bp
Parental seq. overlap (%)	16%
Genomic Region	Intergenic
Retrocopy Summary	FCF1P3, located on chr3:106848655-106849750, is a retrocopy of the parental gene FCF1. Retrocopies of protein-coding genes, also known as processed pseudogenes, are intriguing genomic elements with implications in genome evolution and diseases. While some retrocopies are non-functional, there are examples of retrocopies (retrogenes) acquiring regulatory roles or exhibiting neofunctionalization unrelated to their parental genes.

Parental Gene

Gene Name	FCF1
Full Name	FCF1 rRNA-processing protein
Also known as	Bka\|C14orf111\|CGI-35\|UTP24
Coordinate	chr14:74713118-74738620
Strand	+
Gene summary	Enables RNA binding activity. Predicted to be involved in rRNA processing. Predicted to act upstream of or within endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) and endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to be located in nucleoplasm. Predicted to be part of small-subunit processome. Predicted to be active in nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	FCF1P3
Bonobo	Pan paniscus	FCF1P3
Gorilla	Gorilla gorilla	FCF1P3
Orangutan	Pongo abelii	FCF1P3
Gibbon	Nomascus leucogenys	FCF1P10
Green monkey	Chlorocebus sabaeus	FCF1P7
Crab-eating macaque	Macaca fascicularis	FCF1P4
Baboon	Papio anubis	FCF1P3
Golden snub-nosed monkey	Rhinopithecus roxellana	FCF1P3
Rhesus	Macaca mulatta	Without Homology
Marmoset	Callithrix jacchus	Without Homology
Mouse lemur	Microcebus murinus	Without Homology
Mouse	Mus musculus	Without Homology
Rat	Rattus norvegicus	Without Homology
Chinese hamster	Cricetulus griseus	Without Homology
Rabbit	Oryctolagus cuniculus	Without Homology
Pig	Sus scrofa	Without Homology
Cow	Bos taurus	Without Homology
Sheep	Ovis aries	Without Homology
Dolphin	Tursiops truncatus	Without Homology
Horse	Equus caballus	Without Homology
Dog	Canis familiaris	Without Homology
Panda	Ailuropoda melanoleuca	Without Homology
Cat	Felis catus	Without Homology
Pale spear-nosed bat	Phyllostomus discolor	Without Homology
Velvety free-tailed bat	Molossus molossus	Without Homology
Greater mouse-eared bat	Myotis myotis	Without Homology
Kuhl's pipistrelle	Pipistrellus kuhlii	Without Homology
Greater horseshoe bat	Rhinolophus ferrumequinum	Without Homology
Egyptian rousette	Rousettus aegyptiacus	Without Homology
Sloth	Choloepus didactylus	Without Homology
Tasmanian Devil	Sarcophilus harrisii	Without Homology
Opossum	Monodelphis domestica	Without Homology
Platypus	Ornithorhynchus anatinus	Without Homology
Chicken	Gallus gallus	Without Homology
Turkey	Meleagris gallopavo	Without Homology
Zebra Finch	Taeniopygia guttata	Without Homology
Budgerigar	Melopsittacus undulatus	Without Homology
Painted Turtle	Chrysemys picta	Without Homology
Lizard	Anolis Carolinensis	Without Homology
Frog	Xenopus tropicalis	Without Homology
Zebrafish	Danio rerio	Without Homology
Drosophila	Drosophila melanogaster	Without Homology

Expression

Related Sequence

>FCF1P3
AGAGTGTGGCATGAACATGGGGAAGCAAAATAAAACAGGAAGTATGCGACCATGAAGTGAATGCTTAGTCTCAGAGATCAGAGGCTTAAAGAATAGGATAGACTAAAACGTGAAAAGAAAGAAAAATAGTATCCCAGCATGCTAAAGAAAAGAAAAGTTCCTCAACACCCTTCCTGGTTATTTTTCCAATATAATACACAGCTGGGCCCACCTTACCACATCCTGTTTGACACCAACTTTATCAAATTTTCCATTAAAACCAAACTGGACTTAGTGTAGTCAATGATGGACTGTCTGTATGCCAAGTGTATCCCTTGTATAACTGATTGTGTAATGGCTGAAATTGGGAAATTAGGGCAGAAGTATGGAGCAGCTGTAAGGATTGTTAAGGATCCAATATTAGAATGATTACCGGGGACACACAAAGAAACCTATGCAGATGACAGCTTAGTACAGAGAGTAACTCACAAGTGTTACGTTGTGTCCTTGGTTGACCAGGACCTTAAAAAAAGAATCCAAAAGAATCCTGGAGTTCCTAACACGTACATTTCTAACCATAGATAAAACTCTGAACAGATGTCAGGTGACTATGGAGCCCCTAGGTTCTGCCTCTTATAAGACAAAGTTCCTCTGCCTTTCTTCAACCAACTTTCTATTGTTTCCAGTTCATTAAACATTCAGTAGCATGATATATTCTTCCATTTACCCATTTGCTCTGTTATAAGCTGAGTATGGTTAAATATGCTCACTTTCTGATGCTGTTTTGAAATTGATGTTTTGTCTCATTTAAAAATTTTA

>NM_015962.5
GTAGAAGTATTGCGCCGTTGGTGATTACGGAAGAACCAGGAGTTTGGCGTGACCATGGGGAAGCAAAAGAAAACAAGGAAGTATGCGACCATGAAGCGAATGCTTAGTCTCAGAGATCAGAGGCTtaaagaaaaggatagattaaaacctaaaaagaaagaaaagaaGGATCCCAGCGCATTAAAGGAAAGAGAAGTTCCCCAACACCCTTCCTGCTTATTTTTCCAATATAATACACAGCTGGGCCCACCTTACCACATCCTCGTTGATACCAACTTTATCAACTTTTCCATAAAAGCCAAACTGGACTTAGTGCAGTCAATGATGGACTGTCTGTATGCCAAGTGTATCCCATGTATAACCGATTGTGTAATGGCTGAAATTGAGAAATTGGGGCAGAAGTATCGAGTGGCTCTAAGGATTGCCAAGGATCCAAGATTTGAACGATTACCATGTACACACAAAGGAACCTATGCAGATGACTGCTTAGTACAGAGAGTAACTCAGCATAAGTGTTACATTGTGGCCACAGTTGACCGGGACCTGAAAAGAAGAATCCGTAAGATTCCTGGAGTTCCTATCATGTACATTTCTAACCATAGATACAACATTGAACGGATGCCAGATGATTATGGAGCCCCTCGATTCTAATTCTTACAAGACACAGTTCCTCTGCCTTTCTTCGACCAACTTTCTCTTGTTGCCAGTTCATTACACAAAATGTAGCgggatttttaaggaatcagagagactgatggagttcagggagatatttattatttaggtgcaccagcccagtcagattaacatccaaaggactgaaccctgaacagagttaagttaccttttaagcattttgtggggccgcgggggttggggggaatctgtgcagggggaagcatattacagaagcaagaaagacagttattcaattaactgagacatgcattacatcatttcttacttttcaaggaaaatcatgttttacgacttgagtttatctgtctagttaccttgcagctgcacagctagagaaacagggtatttacaatgcctgggaaaggaggagagataaggctcactagccacagaaaaacaggcagttaatttttaaaggactccagctctttctctttctcacggggaattggattttcttacatgcaactgaatttctgcttacacatttttaaatttcttttaattgcttttccaATGCAATAGCATGAATTATTATTCTGTTGACCTATTTGCCTTACTATGAGCTGAGGGTAGTTCAATATGCTCACTCttttttttttttttcttgagatgaagttttgctctgtcaccaggctggagtgcagtggcgtgatctgggctcactgcaacccctgcctcccatccttcaagtgattctcctgcctcagcctcccgagtagctgggattacaggtacacaccaccatgctcaactaatttttcttttttgggcggggggggtggatatttttagtagagacaaatacttttgtatttttaatacagaaaagtatgcctcggcctcccaaagtgctggaattacagacatgagccactgtgcctggccTGCTCACTTTCTGATGCTGCTTTTTTGTTGtttgtttgtttatttgtttgttttgagacggagtctcgctctgtcaccaggctggagtgcagtggcgcaatctcggctcattgcaacctccgcctcccaggttcaagcgattctcctgcctcagcctgcggagtagctgggactataggtgcgtgccaccacgtccagcCACTGATGCTGTTTTGCCACTGATGCTGTTTTGAAATTGATATTTTGTCTCATAAAAACTAggccaggcatggtggctcattcctgtaatcccagcactttgggaggccaaggtgggtggatcacctgaggtcaggagttggagatgagcctggacaacatggcaaaaccccacctctactaaaaatacaaaaaaaattagctgggtatggtgtcacgtgcctgtaatcccagccactggggaggctgaggcaggagaacctcttgaacccaggaggtggaggttgcagtgagctgagattgcgccactgcattccagcctgggtgacagagtgagactgtctcaaaaaaaaaaaaaaaTTAatgatggtcaaagggtataaaatctcagacaggaagaatatgttttatgctttttttgagttctgttgtacagtgtggtgcctatacttaataatggggtattatacatttcaaaattgatgttctcatcacagaaatgtatttgaagtattgcatatgttaactagcttgatttaactattccatattgtatccacaatttatgatatcactttgtaacccatacatttatacaattataaattgtcaatttacaataaaaAATTTTTGTTGCGTCTTTTTAGAAATCAGATATTCTGATGATTGCTCACATAATTTGGCGGTCATTGTTTTATACTGacttactcaataaacatttattaaatgtatactaggtgcttaataagagatggtcctgccctcaagacactcattatggtgggaaagaaaaacatgtaaatgaataaatgccgtaaaatagcagtgctagggtaaaagtttcagaggcatgtcatgggcacataaaggtggAATGATTTTTTTCTACTGGTTGGGATGGAGAGGGAGGAAAGGCCAGTGGTCATGTGGTTTGAGCTAATCTTAAAAATGAATAGGTGCCTCCCCAGTAAATTAGGAATGGAAGATGAAGCATAGGAAACAGTACACCATAGAAAATCCATTAACCTATGtataatcccagcactttgggagactgaggtgggcagatcacttgaggtcaggagtttgaaaccagcctggccaacatggtgaaaccccacctctactaaaaattccaaaattaactgggcgtggtggtgcaagcctgtagtcccagctacttgggaggctgaggcaggagaatcgcttgaacccgggaggcagaggttgcaacgagccgagatcacgccactgcactccagcctgggcgacagagtgaaactctgtctcaaaaacaaacaaacaaaaaaCCTATGTATTTGTGGGGATTTGGTATATTATTAAGGTGGTATTTCGTTTCTGTGGGAAAAGGAAATTTCATTAACAGGCCAAATAGtctggagtcattctgttagtgttagaatactaattccaccagttaatatctgtatgagttggacaaaccatataaccatctgttgccttccttgtttcctctttaaagtgtttaatccgcaaaacaaacctgataaagtgagattaaattgaatagtacctggcccaagtaagtgttcttcagtaaatgttagtgattattACACAATGGCAAGGTGGCTATCCATTTGAAAAAAAATTAggccgggcgtggtggctcacacctgtaatcccaacactttgggaggccaaggtgggcggatcacctgaggtcaggagcccaagaccagcctgaccaacatggagaaaccccatctctactaaaaatacaaaaaaacaattaggcaggcatggtggcaaatgcctgtattcccagctactctggaggctgaggcaggagaacgcttgaacctgggagatggaggttgtgatgagccgagatcatgccattgcactcattccagcctgggcaacaagagtgaaactctgtctcaaaaaaaaaaaaaaaaaaaGAGAGAGAgaaaaaaattagtttcctacttcacatgattcataaaaatatttcaagtggatcaaagacctaaattttttttttttttgagacagtttctcactctgtcacccaggctgcagtgcgttggcacaatcatgactcactgcagccttgaccttcccaggccctgatgatccaccccagcctctcaagtagctgggatttttgtatttcttacagagatgggattttgccttattgcccaccttggccttctaaagtattgggattatgggcatgagccactgcacccACCCTAAACTTATTTCTAAGCTATGGAAGCATTAGGAAAATAAATGTAAAGAAAAACGTGTTTATCACCTTTGGATAGAATTCTTAAGCAGAATCTAAAAAGATTGAAGAGTTTGAATATATTAAAATTATAGATTTCTGTGCAAGACACTCCCCTCCCCTAAAAAACAAGTGACTGATGAGATTTTCCAATACATGTAACAAGGGTTTAGAGAAATGAGTACTGATGTCATGCTGACAGAAGTGCAAATATTTATGGCCATTTTTTACAGCTGTTGACAAGATCCACTAAAATAAAAATTGCAGATATCCTGTGA

>NM_015962.5 

GTAGAAGTATTGCGCCGTTGGTGATTACGGAAGAACCAGGAGTTTGGCGTGACCATGGGGAAGCAAAAGAAAACAAGGAAGTATGCGACCATGAAGCGAATGCTTAGTCTCAGAGATCAGAGGCTtaaagaaaaggatagattaaaacctaaaaagaaagaaaagaaGGATCCCAGCGCATTAAAGGAAAGAGAAGTTCCCCAACACCCTTCCTGCTTATTTTTCCAATATAATACACAGCTGGGCCCACCTTACCACATCCTCGTTGATACCAACTTTATCAACTTTTCCATAAAAGCCAAACTGGACTTAGTGCAGTCAATGATGGACTGTCTGTATGCCAAGTGTATCCCATGTATAACCGATTGTGTAATGGCTGAAATTGAGAAATTGGGGCAGAAGTATCGAGTGGCTCTAAGGATTGCCAAGGATCCAAGATTTGAACGATTACCATGTACACACAAAGGAACCTATGCAGATGACTGCTTAGTACAGAGAGTAACTCAGCATAAGTGTTACATTGTGGCCACAGTTGACCGGGACCTGAAAAGAAGAATCCGTAAGATTCCTGGAGTTCCTATCATGTACATTTCTAACCATAGATACAACATTGAACGGATGCCAGATGATTATGGAGCCCCTCGATTCTAATTCTTACAAGACACAGTTCCTCTGCCTTTCTTCGACCAACTTTCTCTTGTTGCCAGTTCATTACACAAAATGTAGCgggatttttaaggaatcagagagactgatggagttcagggagatatttattatttaggtgcaccagcccagtcagattaacatccaaaggactgaaccctgaacagagttaagttaccttttaagcattttgtggggccgcgggggttggggggaatctgtgcagggggaagcatattacagaagcaagaaagacagttattcaattaactgagacatgcattacatcatttcttacttttcaaggaaaatcatgttttacgacttgagtttatctgtctagttaccttgcagctgcacagctagagaaacagggtatttacaatgcctgggaaaggaggagagataaggctcactagccacagaaaaacaggcagttaatttttaaaggactccagctctttctctttctcacggggaattggattttcttacatgcaactgaatttctgcttacacatttttaaatttcttttaattgcttttccaATGCAATAGCATGAATTATTATTCTGTTGACCTATTTGCCTTACTATGAGCTGAGGGTAGTTCAATATGCTCACTCttttttttttttttcttgagatgaagttttgctctgtcaccaggctggagtgcagtggcgtgatctgggctcactgcaacccctgcctcccatccttcaagtgattctcctgcctcagcctcccgagtagctgggattacaggtacacaccaccatgctcaactaatttttcttttttgggcggggggggtggatatttttagtagagacaaatacttttgtatttttaatacagaaaagtatgcctcggcctcccaaagtgctggaattacagacatgagccactgtgcctggccTGCTCACTTTCTGATGCTGCTTTTTTGTTGtttgtttgtttatttgtttgttttgagacggagtctcgctctgtcaccaggctggagtgcagtggcgcaatctcggctcattgcaacctccgcctcccaggttcaagcgattctcctgcctcagcctgcggagtagctgggactataggtgcgtgccaccacgtccagcCACTGATGCTGTTTTGCCACTGATGCTGTTTTGAAATTGATATTTTGTCTCATAAAAACTAggccaggcatggtggctcattcctgtaatcccagcactttgggaggccaaggtgggtggatcacctgaggtcaggagttggagatgagcctggacaacatggcaaaaccccacctctactaaaaatacaaaaaaaattagctgggtatggtgtcacgtgcctgtaatcccagccactggggaggctgaggcaggagaacctcttgaacccaggaggtggaggttgcagtgagctgagattgcgccactgcattccagcctgggtgacagagtgagactgtctcaaaaaaaaaaaaaaaTTAatgatggtcaaagggtataaaatctcagacaggaagaatatgttttatgctttttttgagttctgttgtacagtgtggtgcctatacttaataatggggtattatacatttcaaaattgatgttctcatcacagaaatgtatttgaagtattgcatatgttaactagcttgatttaactattccatattgtatccacaatttatgatatcactttgtaacccatacatttatacaattataaattgtcaatttacaataaaaAATTTTTGTTGCGTCTTTTTAGAAATCAGATATTCTGATGATTGCTCACATAATTTGGCGGTCATTGTTTTATACTGacttactcaataaacatttattaaatgtatactaggtgcttaataagagatggtcctgccctcaagacactcattatggtgggaaagaaaaacatgtaaatgaataaatgccgtaaaatagcagtgctagggtaaaagtttcagaggcatgtcatgggcacataaaggtggAATGATTTTTTTCTACTGGTTGGGATGGAGAGGGAGGAAAGGCCAGTGGTCATGTGGTTTGAGCTAATCTTAAAAATGAATAGGTGCCTCCCCAGTAAATTAGGAATGGAAGATGAAGCATAGGAAACAGTACACCATAGAAAATCCATTAACCTATGtataatcccagcactttgggagactgaggtgggcagatcacttgaggtcaggagtttgaaaccagcctggccaacatggtgaaaccccacctctactaaaaattccaaaattaactgggcgtggtggtgcaagcctgtagtcccagctacttgggaggctgaggcaggagaatcgcttgaacccgggaggcagaggttgcaacgagccgagatcacgccactgcactccagcctgggcgacagagtgaaactctgtctcaaaaacaaacaaacaaaaaaCCTATGTATTTGTGGGGATTTGGTATATTATTAAGGTGGTATTTCGTTTCTGTGGGAAAAGGAAATTTCATTAACAGGCCAAATAGtctggagtcattctgttagtgttagaatactaattccaccagttaatatctgtatgagttggacaaaccatataaccatctgttgccttccttgtttcctctttaaagtgtttaatccgcaaaacaaacctgataaagtgagattaaattgaatagtacctggcccaagtaagtgttcttcagtaaatgttagtgattattACACAATGGCAAGGTGGCTATCCATTTGAAAAAAAATTAggccgggcgtggtggctcacacctgtaatcccaacactttgggaggccaaggtgggcggatcacctgaggtcaggagcccaagaccagcctgaccaacatggagaaaccccatctctactaaaaatacaaaaaaacaattaggcaggcatggtggcaaatgcctgtattcccagctactctggaggctgaggcaggagaacgcttgaacctgggagatggaggttgtgatgagccgagatcatgccattgcactcattccagcctgggcaacaagagtgaaactctgtctcaaaaaaaaaaaaaaaaaaaGAGAGAGAgaaaaaaattagtttcctacttcacatgattcataaaaatatttcaagtggatcaaagacctaaattttttttttttttgagacagtttctcactctgtcacccaggctgcagtgcgttggcacaatcatgactcactgcagccttgaccttcccaggccctgatgatccaccccagcctctcaagtagctgggatttttgtatttcttacagagatgggattttgccttattgcccaccttggccttctaaagtattgggattatgggcatgagccactgcacccACCCTAAACTTATTTCTAAGCTATGGAAGCATTAGGAAAATAAATGTAAAGAAAAACGTGTTTATCACCTTTGGATAGAATTCTTAAGCAGAATCTAAAAAGATTGAAGAGTTTGAATATATTAAAATTATAGATTTCTGTGCAAGACACTCCCCTCCCCTAAAAAACAAGTGACTGATGAGATTTTCCAATACATGTAACAAGGGTTTAGAGAAATGAGTACTGATGTCATGCTGACAGAAGTGCAAATATTTATGGCCATTTTTTACAGCTGTTGACAAGATCCACTAAAATAAAAATTGCAGATATCCTGTGA

Publications

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